X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=4723a9a622053fee395cd4f6b69a554a815f4a0a;hb=b482f8156c38c7b5ea498eec33f312375441c352;hp=b40113183b4676c1809f6f1a011ca285c7fbba94;hpb=b25e74cbff1b97e12c1f3b4ea0b1914a13a5c474;p=jalview.git
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-
-
What's new ?
-
-What's new ?
-If you are reading this then you will already have seen some of the recent changes
- made to Jalview.
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window.
-If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:
-
- - Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment creates a "selection region"
- which may be full sequences or groups of residues.
- - To insert or edit the gaps in one sequence in alignment, the "Shift"
- key must be held down when dragging the mouse.
- - To insert or edit gaps for a group of sequences, the "Alt" key
- (or in X windows the "Control" key) must be held down.
- - Selecting colour schemes in the colour menu either sets just the "background"
- colourscheme for the alignment, or - when the tickbox "Apply colour to
- all groups" is ticked, applies the scheme to the background and all groups
- defined on the alignment.
- - Use the right mouse button (apple and click on the Mac) whilst the pointer
- is within the selection area to access the "define" region menu
- to define a new region, give it a name, and change its colourscheme and display
- properties.
- - Conservation is automatically updated whenever the alignment is edited
- - There is no "quick draw" option
- - Edits can be undone, and redone!
-
-
-
- Release |
- New Features |
- Issues Resolved |
-
-
- 2.05b
- 30/8/05 |
-
- - Choose EPS export as lineart or text
- - Jar files are executable
- - Can read in Uracil - maps to unknown residue
- |
-
- - Known OutOfMemory errors give warning message
- - Overview window calculated more efficiently
- - Several GUI bugs resolved
- |
-
-
- 2.05
- 30/8/05 |
-
- - Edit and annotate in "Wrapped" view
- |
-
- - Several GUI bugs resolved
- |
-
-
- 2.04
- 24/8/05 |
-
- - Hold down mouse wheel & scroll to change font size
- |
-
- - Improved JPred client reliability
- - Improved loading of Jalview files
- |
-
-
- 2.03
- 18/8/05 |
-
- - Set Proxy server name and port in preferences
- - Multiple URL links from sequence ids
- - User Defined Colours can have a scheme name and added to Colour Menu
- - Choose to ignore gaps in consensus calculation
- - Unix users can set default web browser
- - Runs without GUI for batch processing
- - Dynamically generated Web Service Menus
- |
-
- - InstallAnywhere download for Sparc Solaris
- |
-
-
- 2.02
- 18/7/05 |
- |
-
- - Copy & Paste order of sequences maintains alignment order.
- |
-
-
- 2.01
- 12/7/05 |
-
- - Use delete key for deleting selection.
- - Use Mouse wheel to scroll sequences.
- - Help file updated to describe how to add alignment annotations.
- - Version and build date written to build properties file.
- - InstallAnywhere installation will check for updates at launch of Jalview.
- |
-
- - Delete gaps bug fixed.
- - FileChooser sorts columns.
- - Can remove groups one by one.
- - Filechooser icons installed.
- - Finder ignores return character when searching. Return key will initiate
- a search.
-
- |
-
-
- 2.0
- 20/6/05 |
- |
- |
-
-
-
-
-
+
+
+
+What's new ?
+
+
+What's new ?
+Highlights in Jalview Version 2.5
+
+ Linked viewing of nucleic acid sequences and structures
+ Automatic Scrolling option in View menu to display the
+ currently highlighted region of an alignment.
+ Order an alignment by sequence length, or using the average score or total feature count for each sequence.
+ Shading features by score or associated description
+ Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).
+ New hide/show options including Shift+Control+H to hide everything but the currently selected region.
+
+Jalview Desktop:
+
+ Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources
+ Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.
+ Group-associated consensus, sequence logos and conservation
+ plots
+ Symbol distributions for each column can be exported and
+ visualized as sequence logos
+ Jalview Java Console
+ New webservice for submitting sequences and IDs to Envision2 Workflows
+ Improved VAMSAS synchronization and sharing of selections.
+
+JalviewLite:
+
+ Middle button resizes annotation row height
+ New Parameters - including default tree display settings.
+ Non-positional features displayed in ID tooltip
+
+Issues Resolved (a select list)
+
+
+ Source field in GFF files parsed as feature source rather
+ than description
+ Non-positional features are now included in sequence feature
+ and gff files (controlled via non-positional feature visibility in
+ tooltip).
+ URL links generated for all feature links (bugfix)
+ Codons containing ambiguous nucleotides translated as 'X' in
+ peptide product
+ Match case switch in find dialog box works for both sequence
+ ID and sequence string and query strings do not have to be in upper
+ case to match case-insensitively.
+ Jalview Annotation File generation/parsing consistent with
+ documentation (e.g. Stockholm annotation can be exported and
+ re-imported)
+ Find incrementally searches ID string matches as well as
+ subsequence matches, and correctly reports total number of both.
+
+ Desktop Issues
+
+ Better handling of exceptions during sequence retrieval
+ PDB files retrieved from URLs are cached properly
+ Sequence description lines properly shared via VAMSAS
+ Sequence fetcher fetches multiple records for all data
+ sources
+ Ensured that command line das feature retrieval completes
+ before alignment figures are generated.
+ Reduced time taken when opening file browser for first time.
+ User defined group colours properly recovered from Jalview projects.
+
+
+
+
+See the Release History page for
+details of all new features and resolved issues.
+
+